Bio::Ontology::GOterm - representation of GO terms
$term = Bio::Ontology::GOterm->new ( -go_id => "GO:0016847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); $term->add_definition_references( @refs ); $term->add_secondary_GO_ids( @ids ); $term->add_aliases( @aliases ); foreach my $dr ( $term->each_definition_reference() ) { print $dr, "\n"; } # etc.
This is "dumb" class for GO terms (it provides no functionality related to graphs). Implements Bio::Ontology::TermI.
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Christian M. Zmasek
Email: czmasek@gnf.org or cmzmasek@yahoo.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address:
Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121
The rest of the documentation details each of the object methods.
Title : new Usage : $term = Bio::Ontology::GOterm->new( -go_id => "GO:0016847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); Function: Creates a new Bio::Ontology::GOterm. Returns : A new Bio::Ontology::GOterm object. Args : -go_id => the goid of this GO term [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a zero-padded integer of seven digits) -name => the name of this GO term [scalar] -definition => the definition of this GO term [scalar] -ontology => the ontology for this term (a Bio::Ontology::OntologyI compliant object) -version => version information [scalar] -is_obsolete => the obsoleteness of this GO term [0 or 1] -comment => a comment [scalar]
Title : init() Usage : $term->init(); Function: Initializes this GOterm to all "" and empty lists. Returns : Args :
Title : GO_id Usage : $term->GO_id( "GO:0003947" ); or print $term->GO_id(); Function: Set/get for the goid of this GO term. This is essentially an alias to identifier(), with added format checking. Returns : The goid [GO:nnnnnnn]. Args : The goid [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a zero-padded integer of seven digits) (optional).
Title : get_secondary_GO_ids Usage : @ids = $term->get_secondary_GO_ids(); Function: Returns a list of secondary goids of this Term. This is aliased to remove_secondary_ids(). Returns : A list of secondary goids [array of [GO:nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits). Args :
Title : add_secondary_GO_id Usage : $term->add_secondary_GO_id( @ids ); or $term->add_secondary_GO_id( $id ); Function: Pushes one or more secondary goids into the list of secondary goids. This is aliased to remove_secondary_ids(). Returns : Args : One secondary goid [GO:nnnnnnn or nnnnnnn] or a list of secondary goids [array of [GO:nnnnnnn or nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits).
Title : remove_secondary_GO_ids() Usage : $term->remove_secondary_GO_ids(); Function: Deletes (and returns) the secondary goids of this Term. This is aliased to remove_secondary_ids(). Returns : A list of secondary goids [array of [GO:nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits). Args :
Title : to_string() Usage : print $term->to_string(); Function: to_string method for GO terms. Returns : A string representation of this GOterm. Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.